I think there are ways other than making your objection part of the public record or letting the topic pass without comment.
As an example, use the interchange recorded in John when Jesus met the woman at the well. He made the point about her living situation, but He did not dwell on it. He had bigger fish to fry. Likewise, He stayed with the woman caught in the act of adultery until all her accusers drifted away. Only when He had her alone did He charge her: Go, and sin no more. The only ones who got His public criticism were those who improperly held themselves up, in public, as examples of holiness and righteousness. He ate and drank with prostitutes and tax collectors, did He not? You have to call a sin a sin, but you also have to meet fellow sinners where they are.
You agree to go to the wedding, but encourage your brother and future sister-in-law to make it a Catholic wedding or to have it blessed by in the Church, should that first opportunity go by. You can encourage them to have their child baptized. You can tell them that you pray for them in their vocations of spouse and parent every day (without making any comments indicating that you coach God about the best way to do that).
Tell them that you are happy that they are marrying and making their commitment to each other public and binding, not just upon each other, but upon everyone else. They are doing a good thing, regardless of whether they are doing everything you might hope. Give them credit for that, and likewise encourage them in all they do that is right, especially if they inspire you in any way.
